Hi, Maybe my message was not understandable enough. I really need your help, so I'll try to be more concise : How do I make a composite output from 2 datatypes that I have declared myself ? I've followed the "Composite Datatypes" wiki but it seems that I've missed something... My composite datatype appears well in "file format" from Get Data's upload file section, but when I run my tool, I have 2 outputs which are the components of my primary datatype, instead of only one output. Best regards, Marine ________________________________ De : Marine Rohmer <marine.rohmer@yahoo.fr> À : "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Envoyé le : Vendredi 8 juin 2012 15h15 Objet : Composite output with self-declarated datatype Hi everyone, I'm trying to add a tool which generates 2 files, that I will call ".xxx" (a text file) and ".yyy" (a binary file) . Both files are needed to use the result of my tool with an other tool I've added. So I wanted to create a composite datatype , that I will call ".composite", whose components are ".xxx" and ".yyy". I've declared the datatype ".xxx", ".yyy" and ".composite" in the datatypes_conf.xml file, and written the required python files . Now, ".xxx", ".yyy" and ".composite" appear in Get Data's "file format" . These are my files : In datatype_conf.xml : <datatype extension="xxx" type="galaxy.datatypes.xxx:xxx" mimetype="text/html" display_in_upload = "True" subclass="True"/> <datatype extension="yyy" type="galaxy.datatypes.yyy:yyy" mimetype="application/octet-stream" display_in_upload = "True" subclass="True" /> <datatype extension="composite" type="galaxy.datatypes.composite:Composite" mimetype="text/html" display_in_upload="True"/> xxx.py (summarized) : import logging from metadata import MetadataElement from data import Text log = logging.getLogger(__name__) class xxx(Text): file_ext = "xxx" def __init__( self, **kwd ): Text.__init__( self, **kwd ) yyy.py (summarized) : import logging from metadata import MetadataElement from data import Text log = logging.getLogger(__name__) # yyy is a binary file, don't know what to put instead of "Text". "Binary" and "Bin" don't work. class yyy(Text): file_ext = "yyy" def __init__( self, **kwd ): Text.__init__( self, **kwd ) composite.py (summarized) : import logging from metadata import MetadataElement from data import Text log = logging.getLogger(__name__) class Composite(Text): composite_type = 'auto_primary_file' MetadataElement( name="base_name", desc="base name for all transformed versions of this index dataset", default="your_index", readonly=True, set_in_upload=True) file_ext = 'composite' def __init__( self, **kwd ): Text.__init__( self, **kwd ) self.add_composite_file( '%s.xxx', description = "XXX file", substitute_name_with_metadata = 'base_name') self.add_composite_file( '%s.yyy', description = "YYY file", substitute_name_with_metadata = 'base_name', is_binary = True ) Atfer having read Composite Datatypes in the wiki, my myTool.xml looks like : <tool id="my tool"> <command> path/to/crac-index-wrapper.sh ${os.path.join( $output_name_yyy.extra_files_path, '%s.yyy')} ${os.path.join( $output_name_xxx.extra_files_path, '%s.xxx' )} $input_file </command> <inputs> <param name="output_name" type="text" value ="IndexOutput" label="Output name"/> <param name="input_file" type="data" label="Source file" format="fasta"/> </inputs> <outputs> <data format="ssa" name="output_name_ssa" from_work_dir="crac-index_output.ssa" label="CRAC-index: ${output_name}.ssa"> </data> <data format="conf" name="output_name_conf" from_work_dir="crac-index_output.conf" label="CRAC-index: ${output_name}.conf"> </data> </outputs> </tool> I have 2 main problems : When I upload a xxx file via "Get Data", there's no problem. However, when I upload a yyy file (the binary one),history bloc rests eternally blue ("uploading dataset") , even for a small file. The second problem is that I want my tool to only generate the .composite file on the history, and not each of .xxx and .yyy. . But when I run my tool I still have 2 outputs displayed in the history : one for xxx and one for yyy. Furthermore, neither of them work, and I have the following message : path/to/myTool-wrapper.sh: 6: path/to/myTool-wrapper.sh.sh: cannot create /home/myName/work/galaxy-dist/database/files/000/dataset_302_files/%s.yyy.xxx: Directory nonexistent path/to/myTool-wrapper.sh: 6: path/to/myTool-wrapper.sh: cannot create /home/myName/work/galaxy-dist/database/files/000/dataset_302_files/%s.yyy.yyy: Directory nonexistent path/to/myTool-wrapper.sh: 11: path/to/myTool-wrapper.sh: Syntax error: redirection unexpected So I've checked manually in /home/myName/work/galaxy-dist/database/files/000/ and there's only "dataset_302.dat", an empty file. (And whatsmore, I don't understand why I get in the message "%s.yyy.xxx" and "%s.yyy.yyy" instead of "%s.yyy" and "%s.xxx" ...) Then I've looked the example of rgenetics.xml, and tried to change the command line and the output : <tool id="my tool"> <command> path/to/myTool-wrapper.sh '$output_name.extra_files_path/$output_name.metadata.base_name' $input_file </command> <inputs> <param name="output_name" type="text" value ="IndexOutput" label="Output name" /> <param name="input_file" type="data" label="Source file" /> </inputs> <outputs> <data format="html" name="output" label="myTool: ${output_name}.html" metadata_source="input_file"/> </outputs> </tool> This gave me : Traceback (most recent call last): File "/home/myName/work/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 59, in run_job job_wrapper.prepare() File "/home/myName/work/galaxy-dist/lib/galaxy/jobs/__init__.py", line 429, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line 1971, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/home/myName/work/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1339157051_58_87978.py", line 83, in respond NotFound: cannot find 'extra_files_path' while searching for 'output_name.extra_files_path' So now I don't know which way is the one to follow : the first one inspired by the example in the wiki, or the second one inspired by rgenetics.xml. And what's wrong with it... I will really appreciate any suggestion ! Best regards, Marine